rs10509305
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_152709.5(STOX1):āc.1824A>Cā(p.Glu608Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 1,614,008 control chromosomes in the GnomAD database, including 37,455 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_152709.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STOX1 | NM_152709.5 | c.1824A>C | p.Glu608Asp | missense_variant | 3/4 | ENST00000298596.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STOX1 | ENST00000298596.11 | c.1824A>C | p.Glu608Asp | missense_variant | 3/4 | 1 | NM_152709.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.176 AC: 26816AN: 152074Hom.: 2866 Cov.: 32
GnomAD3 exomes AF: 0.219 AC: 54508AN: 249390Hom.: 6565 AF XY: 0.220 AC XY: 29723AN XY: 135298
GnomAD4 exome AF: 0.213 AC: 312084AN: 1461816Hom.: 34580 Cov.: 36 AF XY: 0.215 AC XY: 156424AN XY: 727212
GnomAD4 genome ? AF: 0.176 AC: 26835AN: 152192Hom.: 2875 Cov.: 32 AF XY: 0.180 AC XY: 13393AN XY: 74392
ClinVar
Submissions by phenotype
Preeclampsia/eclampsia 4 Pathogenic:1Benign:1
Benign, no assertion criteria provided | curation | Reproductive Health Research and Development, BGI Genomics | Jan 06, 2020 | NM_152709.4:c.1824A>C in the STOX1 gene has an allele frequency of 0.307 in European (Finnish) subpopulation in gnomAD dacabase. 7171 homozygous occurrences are observed in the gnomAD database. This evidence suggests the variant to be classified as benign. ACMG/AMP criteria applied: BA1, BS2. - |
Pathogenic, no assertion criteria provided | literature only | OMIM | May 01, 2005 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | research | H3Africa Consortium | Oct 28, 2020 | While the frequency of the alternate allele in gnoMAD v2.0.2 is 0.06, its frequency in African populations is >5%. This suggests that previous classifications of this variant as pathogenic are in error. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at